## `summarise()` has grouped output by 'patient', 'age_at_sample_exact', 'age_at_sample', 'DOB', 'DATE_OF_DIAGNOSIS'. You can override using the `.groups` argument.
## Joining, by = "PDID"
| patient | ID | age_at_sample_exact | cell_type | phase | BaitLabel | |
|---|---|---|---|---|---|---|
| 2 | PD5163 | PD5163e | 31.87406 | PB Gran | Recapture | PD5163e |
| 3 | PD5163 | PD5163f | 35.59206 | PB Gran | Recapture | PD5163f |
| 1 | PD5163 | COLONY37 | 37.14716 | BFU-E-Colony | Colony | NA |
| 4 | PD5163 | PD5163g | 37.87269 | PB Gran | Recapture | PD5163g |
| 7 | PD5163 | PD5163b4 | 37.87269 | T cell | Recapture | b4 |
| 5 | PD5163 | PD5163h | 40.40246 | PB Gran | Recapture | PD5163h |
| 6 | PD5163 | PD5163b3 | NA | Buccal | Recapture | b3 |
tree=plot_basic_tree(PD$pdx,label = PD$patient,style="classic")
The nodes in this plot can be cross-referenced with nodes specified in subsequent results. The plot also serves to give an idea of what the topology at the top of the tree looks like.
tree=plot_basic_tree(expand_short_branches(PD$pdx,prop = 0.1),label = PD$patient,style="classic")
node_labels(tree)
Note that the different colours on the tree indicate the separately fitted mutation rate clades.
##
## Random-Effects Model (k = 1; tau^2 estimator: REML)
##
## logLik deviance AIC BIC AICc
## -0.0000 0.0000 4.0000 -Inf 16.0000
##
## tau^2 (estimated amount of total heterogeneity): 0
## tau (square root of estimated tau^2 value): 0
## I^2 (total heterogeneity / total variability): 0.00%
## H^2 (total variability / sampling variability): 1.00
##
## Test for Heterogeneity:
## Q(df = 0) = 0.0000, p-val = 1.0000
##
## Model Results:
##
## estimate se zval pval ci.lb ci.ub
## 18.1834 0.3697 49.1795 <.0001 17.4588 18.9081 ***
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
| node | driver | status | child_count | type | colony_count | mean_lambda_rescaled | correction | sd_rescaled | lb_rescaled | ub_rescaled | median_rescaled | p_lt_wt |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| -1 | WT | 1 | -1 | local | 55 | 18.18345 | 1 | 0.1367051 | 17.91952 | 18.45608 | 18.18253 | NA |
| 103 | JAK2 | 1 | 6 | local | 6 | 19.33665 | 1 | 0.6150426 | 18.19465 | 20.61581 | 19.31579 | 0.028325 |
| 110 | DNMT3A | 1 | 8 | local | 8 | 21.52251 | 1 | 0.6723947 | 20.30200 | 22.96595 | 21.48660 | 0.000025 |
| 13 | chrX_DEL | 0 | 1 | local | 1 | 18.98204 | 1 | 3.2404927 | 12.50588 | 26.28242 | 18.75261 | 0.400600 |
All ages are in terms of post conception years. The vertical red lines denote when colonies were sampled and blue lines when targeted follow up samples were taken.
| patient | node | driver | child_count | lower_median | upper_median | lower_lb95 | lower_ub95 | upper_lb95 | upper_ub95 | N | group | age_at_diagnosis_pcy | max_age_at_sample | min_age_at_sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PD5163 | 110 | DNMT3A | 8 | 0.0600579 | 8.307589 | 0.0320775 | 0.1034081 | 6.988003 | 9.928769 | 6 | DNMT3A | 32.00274 | 41.13073 | 32.60233 |
| PD5163 | 103 | JAK2 | 6 | 0.0598308 | 9.276072 | 0.0346673 | 0.1027530 | 7.947406 | 10.747222 | 6 | JAK2 | 32.00274 | 41.13073 | 32.60233 |
Here we exclude all local CNAs and depict as color VAF plots